This is a fairly pointless thread, actually. With 1001 games space on the list, every poster is just naming a game they like, because there's no need to think hard about which games do and don't need to make it on the list.
This actually makes me think, though, of a special edition magazine I picked up several years ago, 'The Best 100 Videogames'. It was printed by gameplayer (www.gameplayer.com.au) and I thought it was a very good read- I still read each full-page (or in the case of the top 10, multi-page) article about each game from time to time. I have also owned, or at least played, a startling percentage of the games on this list. Each game was being judged not only by how good it was at the time, but also how influential and, equally importantly, how well it stands up today without the nostalgia filter and rose-tinted spectacles.
In the interests of sharing, I'll print their list of the top 100 games of all time (remember, this list is several years old by now):
100: Crackdown
99: Psychonauts
98: Sensible Soccer
97: Tekken 3
96: Wipeout
95: God of War
94: Gitaroo Man
93: Paper Mario: the Thousand-Year Door
92: Resident Evil (GC remake)
91: Super Smash Bros Melee
90: Devil May Cry
89: Tomb Raider
88: Sega Rally Championship
87: Mr Driller
86: Outrun 2006 Coast 2 Coast
85: Silent Hill 2
84: Phantasy Star Online
83: NiGHTS Into Dreams
82: Lemmings
81: Robotron 2084
80: Virtua Tennis 3
79: The Secret of Monkey Island
78: Doom 2: Hell on Earth
77: Football Manager 2007
76: Ikaruga
75: Burnout 2: Point of Impact
74: Thief: The Dark Project
73: Puzzle Bobble
72: Killer 7
71: Ninja Gaiden Black
70: Ridge Racers 2
69: Pilotwings 64
68: GTR -FIA GT Racing Game 2
67: Geometry Wars: Retro Evolved
66: F-Zero GX
65: Darwinia
64: System Shock 2
63: Lumines
62: Jet Set Radio Future
61: Manhunt
60: Pac-Man VS
59: Star Fox 64
58: Tempest 2000
57: Soul Calibur
56: Guitar Hero
55: Counter-strike
54: Chrono Trigger
53: Tony Hawk's Pro Skater 2
52: Disgaea: Hour of Darkness
51: Pokemon Ruby/Sapphire
50: Shenmue
49: Animal Crossing
48: Puyo Pop Fever
47: Far Cry
46: Quake III
45: Company of Heroes
44: Super Monkey Ball
43: Bomberman
42: Rome: Total War
41: Gran Turismo 4
40: Warioware, Inc: Minigame Mania
39: Secret of Mana
38: Virtua Fighter 5
37: Starcraft
36: Battlefield 2
35: Metal Gear Solid 2: Sons of Liberty
34: R-Type Final
33: Castlevania: Symphony of the Night
32: Project Gotham Racing 2
31: Katamari Damacy
30: Shadow of the Colossus
29: Deus Ex
28: Perfect Dark
27: Rez
26: Advance Wars
25: SimCity 2000
24: Prince of Persia: The Sands of Time
23: Metroid Prime
22: World of Warcraft
21: Okami
20: Civilization IV
19: Elder Scrolls IV: Oblivion
18: Final Fantasy VII
17: Goldeneye 007
16: Street Fighter Anniversary
15: Pro Evolution Soccer 6
14: Super Mario Kart
13: ICO
12: Grand Theft Auto: Vice City
11: Yoshi's Island
10: Super Metroid
9: Tetris
8: Final Fantasy XII
7: Halo: Combat Evolved
6: Zelda: A Link to the Past
5: Super Mario World
4: Half-Life 2
3: Super Mario 64
2: Resident Evil 4
1: Zelda: Ocarina of Time
While you may not agree with every game on the list and the order may sometimes seem a bit odd, the magazine dedicated a full-page article to explaining each decision. It was really a great list to read and you have to admit it hits pretty much all the essentials (except for games which weren't released when this mag came out 3 years ago, so don't bother complaining). Also note they were only listing 1 (similar) game per franchise- they added Metroid Prime and Super Metroid because they're different genres, while FFVII and FFXII were different enough that they barely count as being part of the same series.
Just food for thought.